Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 2680 to 2729 of 16578 in total
    Value Type  : Ranked
    Filtered  : 1
    Rank
    		Hugo
    		description
    		Network Comparison Type
    		Interaction Map
    		red
    		green
    		network_comparison
    670 RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Subtracted High confidence 232.601 244.534 11.933
    671 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
    CYP3A5 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] Low confidence 203.702 198.095 5.607
    ITGB1 integrin beta-1 precursor (fibronectin receptor beta subunit) (cd29 antigen) (integrin vla-4 beta subunit). [swissprot;acc:p05556] Divided 206.277 200.582 1.02839
    NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] High confidence 210.739 199.398 1.05688
    672 no value dok-like protein. [refseq;acc:nm_024872] Subtracted 216.504 204.622 11.882
    CYP3A7 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] Divided Low confidence 203.727 198.116 1.02832
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Subtracted 204.263 198.663 5.6
    NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided High confidence 210.739 199.398 1.05688
    673 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] 226.497 214.355 1.05664
    CYP3A4 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Subtracted Low confidence 203.747 198.152 5.595
    DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Divided 203.604 197.996 1.02832
    DOK2 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Subtracted High confidence 216.504 204.622 11.882
    674 no value adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Low confidence 205.207 199.613 5.594
    DOK1 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] High confidence 216.504 204.622 11.882
    HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Divided 226.497 214.355 1.05664
    PRSS7 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Low confidence 204.81 199.174 1.0283
    675 CYP3A5 cytochrome p450 3a5 (ec 1.14.14.1) (cypiiia5) (p450-pcn3). [swissprot;acc:p20815] 203.702 198.095
    FRK tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Subtracted High confidence 216.504 204.622 11.882
    PRPF31 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Low confidence 201.821 196.233 5.588
    SIM1 single-minded homolog 1. [swissprot;acc:p81133] Divided High confidence 226.497 214.355 1.05664
    676 DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Low confidence 202.698 197.124 1.02828
    MRTO4 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Subtracted High confidence 245.84 257.636 11.796
    POLR2G dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Divided 232.469 245.613 1.05654
    RABEP1 rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Subtracted Low confidence 198.493 192.907 5.586
    677 CCDC53 protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0] Divided 207.03 201.339 1.02827
    DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] Subtracted 202.698 197.124 5.574
    FBL fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] High confidence 245.246 233.483 11.763
    LSM4 u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Divided 228.944 216.745 1.05628
    678 AP1S1 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Subtracted Low confidence 205.169 199.601 5.568
    CYP3A4 cytochrome p450 3a4 (ec 1.14.13.67) (quinine 3-monooxygenase) (cypiiia4) (nifedipine oxidase) (nf-25) (p450-pcn1). [swissprot;acc:p08684] Divided 203.747 198.152 1.02824
    PPIL4 peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Subtracted High confidence 226.135 214.405 11.73
    SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] Divided 208.482 220.175 1.05609
    679 no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 132.413 125.389 1.05602
    ERBB4 receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Subtracted Low confidence 211.36 205.793 5.567
    SNX5 sorting nexin 5. [swissprot;acc:q9y5x3] High confidence 208.482 220.175 11.693
    YEATS4 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] Divided Low confidence 198.424 192.974 1.02824
    680 EDEM2 putative alpha-mannosidase c20orf31 precursor (ec 3.2.1.-). [swissprot;acc:q9bv94] 196.228 190.844 1.02821
    ERBB3 receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Subtracted 211.36 205.793 5.567
    HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided High confidence 132.413 125.389 1.05602
    SFRS18 sr rich protein. [refseq;acc:nm_032870] Subtracted 225.293 213.64 11.653
    681 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Divided Low confidence 206.115 200.462 1.0282
    HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] High confidence 132.413 125.389 1.05602
    IFRD1 interferon-related developmental regulator 1 (nerve growth factor- inducible protein pc4). [swissprot;acc:o00458] Subtracted Low confidence 204.538 198.974 5.564
    SNW1 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 220.593 208.987 11.606
    682 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 132.413 125.389 1.05602
    DDX54 atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Low confidence 204.263 198.663 1.02819
    NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Subtracted High confidence 246.055 234.458 11.597
    SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Low confidence 200.62 195.059 5.561
    683 CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Divided 216.618 210.69 1.02814

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/